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When upgrading to 2019.1, the content of my Python tool was deleted. Although this may be a bug in the 2019.1 version, or just a bug in the upgrade process. Either way, it is problematic that details of a canvas would be deleted at all.
My guess is if the content of the Python Tool could be reliably stored in the canvas XML this issue could potentially be resolved.
I ran into a similar issue yesterday. One of my teammates, @MichaelSu , suggested creating a copy of the workflow and changing the file extension from ".yxmd" to ".txt". Open the text file. You should be able to see the XML code for that workflow, including your python code. I ended up creating a new copy of my workflow, deleted the python tool, and added a clean Python tool.
There is currently a defect in Designer that will wipe/reset all code in a canvas's Python tools if the canvas also has a macro with an embedded Python tool. We have been able to replicate this issue. This would be a very desirable fix as it would greatly increase the effectiveness of our solutions